[phenixbb] not enough memory error in Resolve/AutobuildWizard

Tatyana Sysoeva tatyanasysoeva at gmail.com
Fri Jun 5 11:58:31 PDT 2009


thank you, will do, will see what happen

On Fri, Jun 5, 2009 at 2:37 PM, Tom Terwilliger <terwilliger at lanl.gov>wrote:

> Hi Tatiana,
> Thanks for trying running the "temporary.com" file directly.  The fact
> that it runs means that your machine has no problem doing this job, at least
> in principle.
>
> The installation problem you had with 1.4-85 is a problem we are currently
> trying to debug, as Ralf just replied to you about...
>
> I am guessing that the run of autobuild has the same problem of deletion of
> files.
>
> Can you try running your exact same job on a single machine with local
> disk, to see if it will run properly in this case?
>
> All the best,
> Tom T
>
> On Jun 5, 2009, at 12:05 PM, Tatyana Sysoeva wrote:
>
>
> On Wed, Jun 3, 2009 at 12:27 PM, Thomas C. Terwilliger <
> terwilliger at lanl.gov> wrote:
> Hi Tatiana,
>
> This may be a little difficult to debug on a cluster...but here goes.
>
> The error message you got comes from
>
> AutoBuild_run_1_/TEMP0/
>>
>> AutoBuild_run_1_/TEMP0/temporary.com
>>
>> You can see exactly what happens with that command file if you can log on
>> to a machine in the cluster:
>>
>> cd AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/TEMP0
>>
>> then copy temporary.com to test.com and edit test.com to replace all the
>>  material at the top of the file after #!/bin/csh -f (something like this
>> below) all the way down to "outputdir":
>>
>> delete all this:
>> -------------
>> setenv CCP4_OPEN UNKNOWNsetenv SOLVEDIR
>> /Users/terwill/unix/PHENIX/phenix-1.4-67/solve_resolve/ext_ref_files
>>  setenv SYMOP
>> /Users/terwill/unix/PHENIX/phenix-1.4-67/solve_resolve/ext_ref_file
>>  s/symop.lib
>> /Users/terwill/unix/PHENIX/phenix-1.4-67/build/mac-intel-
>> osx/solve_resolve/exe/r
>>  esolve <<EOD > AutoBuild_run_1_/TEMP0/image.log
>> access_file mirima.dat
>> workdir AutoBuild_run_1_/TEMP0
>> outputdir /Users/Shared/unix/transfer/shiven/AutoBuild_run_6_
>> -------------
>>
>> replace with:
>>
>> phenix.resolve --huge <<EOD
>>
>> and then run ./test.com ....it should bomb and tell you what is wrong.
>>
>> It is possible that the size of your problem is too big for even the 8 GB
>> of memory on your machine, but that would imply a pretty big cell and
>> moderate or high resolution.  Hopefully the output of that test will tell
>> you...
>>
>> Just to be sure, you might also go to the phenix web site and download a
>> recent "nightly build" to make sure that there is not some other type of
>> problem going on.
>>
>> All the best,
>> Tom T
>>
>>
> Good afternoon!
>
>
> Thank you so much for the reply.
> I edited temporary.com and ran it, it reported no error.
>
> when I'm installing phenix 1.4-85, it stops at
> *.................................
>       converting reflection_file_tools.html to reflection_file_tools.raw
>       converting reflection_statistics.html to reflection_statistics.raw
>       converting xtriage_gui.html to xtriage_gui.raw
>       converting raw HTML files, creating tables-of-contents, and indexing
> *
>
> for "infinite" time. After Ctrl-C it continued and finished installation.
> I tried to run phenix.autobuild and it hangs
>
> in gui-output.log -
> *STEP: ImportRawData_output_files  Run 1
> List of files to convert to mtz format:
> File 1: e239a.hkl*
>
> in autobuild_run1.log -
> *ImportRawData_output_files  ImportRawData  Run 1 Thu Jun  4 21:54:11 2009
> summary of input files:
> hklin : /home2/tas354/phenix_runs/20090603/e239a.hkl
>     input labels:["FOBS", "SIGMA"]
>     OUTPUT FILE NAME:
> /home2/tas354/phenix_runs/20090603/ImportRawData_run_1_/e239a_PHX.mtz
> SPACE GROUP NAME: P 21 21 2
>  CELL: [251.209, 242.58600000000001, 40.703000000000003, 90.0, 90.0, 90.0]
>
> *and after that it does not quit and seems to be doing nothing new for the
> rest of the available time.
>
>
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>
>
>
> Thomas C. Terwilliger
> Mail Stop M888
> Los Alamos National Laboratory
> Los Alamos, NM 87545
>
> Tel:  505-667-0072                 email: terwilliger at LANL.gov
> Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
> PHENIX web site: http:www.phenix-online.org
> ISFI Integrated Center for Structure and Function Innovation web site:
> http://techcenter.mbi.ucla.edu
> TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
> CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
>
>
>
>
>
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